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Annually, the Hinton Lab at the Institute of Integrative Biology invites A-level students to spend time learning new skills whilst working on a chosen project within our research lab. This year, the Hinton Lab Intern Week continued its collaboration with Dr Adam Roberts from the Liverpool School of Tropical Medicine and focused on the “Swab and Send” project, which aims to combat the very real threat that antimicrobial resistance poses to our health. The students looked for new antibiotic-producing bacteria by swabbing toys belonging to children of different age groups.

Over the course of the week of 23 July 2018, the four interns, supervised by PhD students Wai Yee Fong and Xiaojun Zhu, learned techniques that included making media for agar plates, inoculating bacteria, gram staining and microscopy. They also visited various parts of the Institute and the Liverpool School of Tropical Medicine. By the end of the week, the students had made some promising discoveries, and identified several new potential antibiotic-producing bacteria.

Sharing their thoughts and reflections on the Intern Week, the students said the following:

Michael Campbell: “I enjoyed the agar art session the most as it was fun and interesting to draw pictures using different types of bacteria. I also found the tours of the IIB genomics facilities and Centre for Cell Imaging very interesting.”

Catherine Lowe: “It was interesting to see the different parts of the Institute and how they worked together, and how the lab works. I really enjoyed working in a research lab and doing something more than the theory which is all that we covered at school.”

Niamh Emond: “What I liked about the Intern Week was getting the opportunity to do practical lab work that can potentially make a difference.”

Professor Hinton said: “It’s been a pleasure to welcome the next generation of scientists to work in our lab. It was inspiring to see the levels of interest of these students as they take on quite a challenging set of experiments. By teaming up with the ‘Swab and Send’ project, the students could discover bacteria that produce novel antibiotics. We are very grateful for the help of Adam Roberts, and for the financial support from the Wellcome Trust, which allows my lab to run this Intern Week”.

An innovative schools outreach programme that encourages students to think about sustainable food production is set to return after a successful first run earlier this year.

Future Food Challenge, a 12 week programme delivered by social enterprise Farm Urban and the University’s Institute of Integrative Biology, challenges Year 9 students to think up new ideas for growing food in urban environments using aquaponics – a sustainable method of raising both fish and vegetables.

The programme, funded by Shaping Futures, the Merseyside partner for the National Collaborative Outreach Programme (NCOP), gives school teams the chance to immerse themselves in the science of aquaponics with their very own Farm Urban Produce Pod system, before forming their own start-up, developing a business idea and designing and building their own aquaponic food system.

The programme provides students with the opportunity to gain an insight into start-up businesses, social enterprise and how they link into Higher Education activity, whilst developing skills in project management, leadership, finance, teamwork, communication and scientific research.

This year’s finale event, held at Farm Urban’s agri-lab space at the Liverpool Life Sciences UTC in July, gave teams the opportunity to exhibit their work, display their systems and pitch their business idea to a panel of judges, comprised of local business leaders and university academics.

Business ideas ranged from systems for use in primary schools to hospitals and local cafes. The overall winners from Woodchurch High School in Wirral carried out research and spoke to local charities and churches to create a system that would provide fresh food for those accessing food banks. The winning team said: “We have loved our aquaponics journey from fish to free fresh food for everyone. It has made us more aware of food problems people face and how to help them using science.”

Dr Iain Young, University lead for the programme commented: “Teaming up with organisations outside the University can be a really powerful way of delivering public engagement, showcasing our science and involving the public in research. This project gave us the opportunity to partner with Farm Urban to reach hundreds of school children from less advantaged backgrounds. Farm Urban are an inspiration in themselves, promoting local, healthy food production, and they also deliver exceptional events and programmes. I have found the whole experience of working with them on this project very rewarding.”

Farm Urban is now encouraging the Future Food Challenge teams to act as Future Food Ambassadors, sharing what they’ve learnt and inspiring their fellow students to think about what they can do collectively to continue to tackle global food challenges in their own communities.

On Tuesday 28th August, six members from the Centre for Proteome Research held a Victoria Gallery and Museum Summer Science Club session for local primary school children. The session, entitled ‘Marvellous Molecules’, began with a messy activity where the children were able to explore the components of ‘blood’. We used water beads, ping pong balls and square pieces of sponge to represent the red blood cells, white blood cells and platelets, respectively. The three components were bathed in water to represent blood plasma. All four components were correctly identified by the children and they even knew all the functions!

We then went on to explain that blood cells contain DNA sequences and that these sequences can be used to make proteins in our body. The children each selected a blood cell from the ‘blood’ mixture and opened them to reveal a laminated DNA sequence that coded for a different protein from different organisms. For example we had the DNA code for a protein in the venom of a cobra and the protein that causes oranges to ripen. Using this code the children could create DNA code bracelets where each nucleobase corresponded with a particular colour of bead. After creating the parent strand, using base coding pairs, the children were able to create the daughter strand. The children enjoyed this so much some made up to three bracelets!

Next we moved onto ‘DNA whispers’. This was a Chinese whispers activity using sentences about DNA to explain how it can sometimes be copied incorrectly causing errors. Some changes often don’t cause a problem, however, other errors (or mutations) can cause genetic diseases such as sickle cell anaemia. One of the sentences used in the game was “Even identical twins don’t have identical DNA” which got changed to “Even identical twins don’t have DNA”, proving a point about how small changes can have a big effect on the meaning of the sentence, or in terms of proteins, their function. We explained about sickle cell anaemia and the children were able to mix some blue water beads into the ‘blood’ mixture, representing the less oxygenated sickle cells. We explained that people with sickle cell anaemia can experience pain, but using some ‘marvellous molecules’ we can treat these symptoms. We looked at the structure of three of these molecules; paracetamol, ibuprofen and aspirin and got the children to make the structures out of paper and pipe cleaners.

We finished the session by asking the children questions about what they had learnt during the session. They were able to answer every question and were awarded with stickers for the correct answers.

We were all very impressed by the knowledge and enthusiasm of the children that attended the session and we look forward to helping out again next year!

With the help of IIB’s Johnston Postdoctoral Development Fund, I was able to visit a world-leading lab in Denmark in order to enhance my knowledge of advanced synthetic biology techniques. Prof Mortensen’s lab is situated at the technical University of Denmark (DTU) located in Lyngby, just outside central Copenhagen. The Johnston Fund kindly covered costs for my travel and AirBnB accommodation close to the DTU, giving me almost two weeks to experience life working at the DTU and learning novel molecular biology techniques.

The key aim of my trip was to learn the ‘tricks of the trade’ of Uracil-Specific Excision Regent (USER) cloning, a technique which multiple scientists at the university have struggled to utilise. In principle, USER cloning should be a straight forward one-pot cloning reaction which holds several advantages over other traditional and more modern cloning methods. Specifically, USER cloning utilises a ligation-free protocol, generates highly specific sticky ends and does not rely on the presence of restriction enzyme recognition sequences. The premise of USER cloning is that by incorporating a single deoxyuracil around 8-12 bases from the 5’ end of each primer, highly specific and long sticky ends can be created on the resulting PCR product with the USER enzyme mix. USER enzyme contains uracil DNA glycosidase (UNG) which excises uracil nucleotides from PCR products and DNA glycosylase-lyase endo VIII which releases the sequence upstream of the uracil nucleotide. The overhangs created are sufficiently long that DNA assembled into a circular plasmid is suitably stable to be transformed into bacteria without prior ligation.

My visit to Prof Mortensen’s lab gave me hands on experience of USER cloning alongside established experts in the field of cell factory construction and engineering. Whereas my expertise lies mainly with the use of bacteria for the production of heterologous proteins and secondary metabolite pathways, Prof Mortensen’s lab focuses on yeast and fungi such as Aspergillus. The main focus of the lab is the discovery of valuable products from fungi and the development of optimal cell factories for their production. To this end, they use CRISPR technology both to insert gene pathways into the organism of interest and to regulate the pathway to give optimal output of the desired molecule.

I was lucky enough to work alongside Dr Katherina Vanegas Garcia who developed “SWITCH” and “TAPE” techniques to help speed up strain construction when developing yeast cell factories. Using these techniques strains can be generated that can iteratively switch between a genetic engineering and a pathway control state. For instance a multi-gene pathway can be inserted into an innocuous location in the genome of the desired strain using Cas9 nuclease in genetic engineering mode. Subsequently the cell factory can be switched into the pathway control state using a dCas9 mutant to up or down regulate different genes in the pathway and monitor the effects to optimise final product yield. She also helped developed a Technique to Assess Protospacer Efficiency (TAPE) whereby the efficiency of particular sgRNA protospacer sequences are assessed for their efficiency to target Cas9 to genomic DNA and cause double strand breaks. The principle is that double strand breaks are lethal in yeast and therefore the efficiency of a protospacer sequence should be reflected in the survival rate of transformants in the absence of a repair template. This technique is also applicable in Aspergillus nidulans NID1 strain which is deficient for non-homologous end joining and hence double strand breaks will also be lethal in this strain.

I designed two experiments to test the application of USER cloning for future use in GeneMill. The first was to assemble 5 stretches of DNA encoding an operon of 13 genes and spanning almost 14 kilobases. USER overhangs were designed to assemble these genes into a USER backbone developed by Dr Vanegas Garcia. Unfortunately, a plasmid encoding all 13 genes was not obtained from these experiments, however, staff and students at the DTU have succeeded in cloning large gene constructs in this manner. Presumably there is an issue with the specific DNA sequence used in this construct which has also proved problematic when using other cloning techniques in the past.

The second experiment was to clone three sgRNA protospacer sequences into a USER backbone designed for CRISPR in Aspergillus nidulans. This cloning was successful on the first attempt and subsequently I was able to carry out CRISPR TAPE experiments to assess the efficiency of targeting of the protospacer sequences to my gene of interest in A. nidulans. All three sgRNA constructs were lethal in NID1 strain when compared to the control transformation showing that all three protospacer sequences were highly efficient. In parallel, I also transformed each sgRNA along with a repair oligo to insert single amino acid changes in my gene of interest. Unfortunately, all three transformants were extremely sick with only one colony from one sgRNA proving viable. This could indicate either that the mutations encoded by the rescue oligos were also lethal or repair using the rescue oligo was not achieved. Without viable transformants to PCR from this is difficult to check. Instead I plan to design oligos encoding silent mutations in the hope that I will then obtain viable transformants.

In summary, my visit to the DTU gave me the opportunity to test USER cloning in both challenging and simple applications. I was also able to conduct a series of CRISPR experiments in A. nidulans, an organism with which I had no prior experience. In addition to receiving hands-on training in the lab, I was given the opportunity to speak to members of different research groups and attend a number of research seminars during my stay. Research areas ranged from discovery of novel antibiotics in fungi to pleasant smelling moss that can be used as an alternative to air freshener! Of particular interest was the Diversify project which is a huge collaboration between many different researchers at the DTU and industrial partners Novozymes and Novo Nordisk. This project aims to take hundreds of yeast and fungal strains and adapt them for the aforementioned SWITCH technique by identifying innocuous sites for heterologous pathway integration. These strains can then be rapidly screened for optimal production of desired metabolites. Ambitious, high throughput, multi-partner, synthetic biology challenges such as this have the ability to change the wider approach to industrial biotechnology enabling sufficient production of useful or valuable compounds that would otherwise be ignored due to underperforming host strains.

I have been extremely privileged to have been selected for receipt of the Johnston Fund and as a consequence I have obtained invaluable experience of how another synthetic biology-focused research lab works. I have renewed enthusiasm that synthetic biology can revolutionise biological research and has the potential to have a significant impact on how we think about the future of industrial biotechnology. Not only am I now equipped to teach and supervise students and colleagues about how to utilise USER cloning, the visit to Denmark has given me a wider perspective on how to approach various industrial projects with which I am involved. I therefore believe that the experience has greatly enhanced my professional development and will aid my productivity across all aspects of my work.

The annual Family Science Fair, held during British Science Week on the 10th March, was one of Ness Botanic Gardens’ largest public engagement events. This year, the event attracted over 1000 visitors. Amongst these, many families took the opportunity to visit Ness, and came in for an afternoon of fun, science-oriented hands-on activities, demonstrations or talks. Members of Raj Whitlock’s research group (Christoph Hahn, Di Yang, Toby Irving, Yuan-Fu Chan) ran a stall themed around “Plants, Microbes and Climate Change”. Both kids and “bigger kids” learned about soil microbes and where they live, what they do, but also how climatic changes might affect belowground ecosystems. We introduced some of the most important soil microbial species that help to maintain the health of plants, using an interactive poster. One of our aims was to reveal the belowground world of soil as an interacting and extremely diverse network of microbes that has strong effects on the plants above. To help our visitors understand how this belowground world fits together, we prepared observation pots (“rhizotrons”) and a big tank containing plants rooted into see-through Phytagel. Visitors of all ages were amazed to see intricate the root networks of plant roots growing into a translucent gel. Many visitors also took part in a competition to guess the number of microbes present in 1 g of soil, with a chance to win a cuddly toy (plushy) version of the common cold or flesh-eating disease. The day was an extremely positive one, and widely appreciated by visitors, some of whom did not want to leave the exhibition! There is just under one year to wait until the next Family Science Fair at Ness…

The Merseyside Young Life Scientists scheme offers an exciting series of events for Year 12 students interested in learning more about a career in life sciences.
Whilst most students were enjoying their Easter Break, 30 Year 12 students who are part of Merseyside Young Life Scientists were up early making their way to the School of Life Sciences for a Becoming Scientists Taster Day.
Students were able to experience a first year lecture on DNA and spend time in the teaching labs. Lecturers, Postgraduate students and Undergraduate students were on hand to show these year 12 students what being an undergraduate in life sciences is really like.

After a busy morning, of lectures and practical laboratory experiments students caught up with their PhD mentors over lunch. Choosing a topic to research for the academic poster presentation is the next challenge for the students.
Over the next few months, students on the scheme will produce posters on a scientific topic with the help of their PhD student mentors. The culmination of their hard work will be a Merseyside Young Life Scientists conference showcasing their posters in September.

Thanks to everyone who helped out with the Becoming Scientists Taster Day!

Dr Simon Maher (EEE) with Dr Iain Young (IIB) and Prof Joe Spencer (EEE) in Thailand last week as part of an Institutional Links Award with Chulalongkorn University where they delivered a workshop Advancing Food Security with Sensors and Analytical Instrumentation to staff and students from Chulalongkorn University and representatives from leading Thai biotechnology and food companies. They also provided their partners on the Award, Dr Thanit Praneenararat and Prof. Tirayut Vilaivan, a prototype bespoke portable Ion Mobility Spectrometer to test for antibiotics in food utilizing technologies developed jointly with the partners. While in Thailand, the group met with several companies in the global food industry including senior managers from the CP Group (seen in the picture), a global conglomerate with revenues > $45 billion USD. The plan is to expand the utility of the devices for the food and biotechnology sector and to expand its capability to include detection and quantification of antibiotics and other pharmaceuticals, food-borne pathogens and other contaminants.